rs984298

Variant names:

• chr13-108803822-A-G
• rs984298
• NM_001198950.3:c.742-2857A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-108803822-A-G
• chr13-108803822-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001198950.3(MYO16):​c.742-2857A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,038 control chromosomes in the GnomAD database, including 40,804 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40804 hom., cov: 32)
• Consequence: MYO16 NM_001198950.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 0 publications found

Genes affected

MYO16 (HGNC:29822): (myosin XVI) This gene encodes an unconventional myosin protein. The encoded protein has been proposed to act as a serine/threonine phosphatase-1 targeting or regulatory subunit. Studies in a rat cell line suggest that this protein may regulate cell cycle progression. A variant within this gene may be associated with susceptibility to schizophrenia and elevated expression of this gene has been observed in the frontal cortex of human schizophrenia patients. [provided by RefSeq, Mar 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO16	NM_001198950.3	c.742-2857A>G		intron_variant	Intron 6 of 34	ENST00000457511.7	NP_001185879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO16	ENST00000457511.7	c.742-2857A>G		intron_variant	Intron 6 of 34	1	NM_001198950.3	ENSP00000401633.3
MYO16	ENST00000356711.7	c.676-2857A>G		intron_variant	Intron 6 of 34	1		ENSP00000349145.2
MYO16	ENST00000251041.10	c.676-2857A>G		intron_variant	Intron 6 of 24	5		ENSP00000251041.5
MYO16	ENST00000375857.6	n.62-2857A>G		intron_variant	Intron 1 of 21	2

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109439 AN: 151920 Hom.: 40770 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.742

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.720 AC: 109524 AN: 152038 Hom.: 40804 Cov.: 32 AF XY: 0.728 AC XY: 54126 AN XY: 74302

African (AFR) AF: 0.523 AC: 21669 AN: 41452

American (AMR) AF: 0.801 AC: 12231 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2935 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5164 AN: 5168

South Asian (SAS) AF: 0.881 AC: 4241 AN: 4816

European-Finnish (FIN) AF: 0.833 AC: 8798 AN: 10566

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51866 AN: 67974

Other (OTH) AF: 0.745 AC: 1574 AN: 2112

Alfa AF: 0.690 Hom.: 17229

Bravo AF: 0.709

Asia WGS AF: 0.911 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.34
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs984298; hg19: chr13-109456170;